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auto3dem:documentation [2015/07/08 12:49]
gcardone
auto3dem:documentation [2019/06/19 16:22] (current)
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   * [[auto3dem:​install|Installation]]   * [[auto3dem:​install|Installation]]
  
-  * [[auto3dem:​userguide|User Guide]] ​([[http://​cryoem.ucsd.edu/​programs/​auto3dem_usersguide_v4.04.pdf|PDF]]) ([[http://​cryoem.ucsd.edu/​programs/​auto3dem_usersguide_v4.04.htm|HTML]])+  * [[auto3dem:​userguide|User Guide]] 
 + 
 +  * [[auto3dem:extra_tools|Auxiliary ​programs]]
  
   * Protocols   * Protocols
-    * [[auto3dem:​documentation:​protocols:​initial_model|Generate ​a starting model]]+    * [[auto3dem:​documentation:​protocols:​initial_model|Generating ​a starting model]] 
 +    * [[auto3dem:​documentation:​protocols:​focused_refinement|Mask-focused refinement]]
     * [[auto3dem:​documentation:​protocols:​asymmetric_reconstruction|Asymmetric reconstruction]]     * [[auto3dem:​documentation:​protocols:​asymmetric_reconstruction|Asymmetric reconstruction]]
     * [[auto3dem:​documentation:​protocols:​gold_standard|Gold Standard procedure]]     * [[auto3dem:​documentation:​protocols:​gold_standard|Gold Standard procedure]]
  
   * Documentation for the parallel programs called by Auto3DEM (PDFs) [:!: last updated Oct 2004]   * Documentation for the parallel programs called by Auto3DEM (PDFs) [:!: last updated Oct 2004]
-    * [[http://cryoem.ucsd.edu/​programs/​p3dr.pdf|P3DR]] 3D image reconstruction +    * [[http://bakerlab.ucsd.edu/​programs/​p3dr.pdf|P3DR]] 3D image reconstruction 
-    * [[http://cryoem.ucsd.edu/​programs/​pcut.pdf|PCUT]] Cutting spherical annulus from map +    * [[http://bakerlab.ucsd.edu/​programs/​pcut.pdf|PCUT]] Cutting spherical annulus from map 
-    * [[http://cryoem.ucsd.edu/​programs/​por.pdf|POR]] Local refinement of image origins and orientations +    * [[http://bakerlab.ucsd.edu/​programs/​por.pdf|POR]] Local refinement of image origins and orientations 
-    * [[http://cryoem.ucsd.edu/​programs/​pftsearch.pdf|PPFT]] Local refinement of image origins and orientations +    * [[http://bakerlab.ucsd.edu/​programs/​pftsearch.pdf|PPFT]] Local refinement of image origins and orientations 
-    * [[http://cryoem.ucsd.edu/​programs/​psf.pdf|PSF]] Structure factor determination and FSC calculation+    * [[http://bakerlab.ucsd.edu/​programs/​psf.pdf|PSF]] Structure factor determination and FSC calculation
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 ==== RobEM === ==== RobEM ===
  
-  * User's Guide ([[http://cryoem.ucsd.edu/​programs/​robem_usersguide_v4.01.pdf|PDF]]) ([[http://cryoem.ucsd.edu/​programs/​robem_usersguide_v4.01.htm|HTML]])+  * User's Guide ([[http://bakerlab.ucsd.edu/​programs/​robem_usersguide_v4.01.pdf|PDF]]) ([[http://bakerlab.ucsd.edu/​programs/​robem_usersguide_v4.01.htm|HTML]])